Genetic Subtypes and Outcome of Patients Aged 1 to 45 Years Old With Acute Lymphoblastic Leukemia in the NOPHO ALL2008 Trial

Ulrika Norén-Nyström1,*, Mette K. Andersen2, Gisela Barbany3, Vaidas Dirse4, Martine Eilert-Olsen5, Marie Engvall6, Arja Harila-Saari7, Mats Heyman8,9, Randi Hovland10, Satu Häikiö11, Jón J. Jónsson12,13, Ritva Karhu14, Eigil Kjeldsen15, Anna Norberg16, Birgitte S. Preiss17, Kati Pulkkinen18, Petter Quist-Paulsen19, Hannele Räsänen20, Kjeld Schmiegelow21, Anne Seitsonen22, Helene Sjögren23, Pille Tammur24, Bertil Johansson25,26,*

Clinical    After an amendment in 2009, ETV6::RUNX1-positive ALL cases with WBC counts ≥100 × 10 9 /L received prednisolone instead of dexamethasone; hence, only the 6 initial cases with hyperleukocytosis were stratified to Dexa induction.
c Comprises patients who died during induction, were lost to follow-up, abandoned protocol therapy before day 29, or had received such a modified therapy that they were considered outliers.
BCP  Of the 278 T-cell ALLs, 18% were genetically normal, 71% abnormal, and 11% uninformative; these did not differ with respect to clinical findings at diagnosis, risk stratification, or outcome (Suppl . Table S2), in line with previous studies. 7 Importantly, however, the outcome of T-cell ALL clearly improved compared with the previous NOPHO ALL2000 trial 8,9 and several other trials (Suppl . Table S3). Eight (2.9%) patients had KMT2A-r-positive T-cell ALL (Suppl. Table S4) and 7 of them are alive in complete remission 1 (CR1) (1 patient succumbed to treatment-related toxicity), suggesting that the prognosis of KMT2A-r-positive T-cell ALL may be relatively favorable. However, international collaborations are required to analyze a sufficiently large number of cases to be able to address the prognostic implications of KMT2A-r in T-cell ALL.
The pCIR, pDFS, pEFS, and pOS were particularly favorable for patients with HeH, ETV6::RUNX1, or TCF3::PBX1 (Table 1, Figure 1, Suppl. Figures S1-S4, and Suppl. Table S5). These groups had 5-year pOS of ≥0.96; similar survival rates have been reported in recent treatment trials (Suppl . Tables  S6-S8). Interestingly, the excellent outcome of the HeH and ETV6::RUNX1 groups was achieved by SR chemotherapy in 67% of the patients. In fact, some of the patients may have been overtreated already by that treatment, as indicated by the nonnegligible frequency (~2.2%) of death in CR1 or second malignant neoplasm in the SR group (Suppl . Table S9).
Although dic(9;20)(p13;q11) does not result in a specific gene fusion and sometimes occur together with bona fide primary gene fusions, such as BCR::ABL1, 10,11 it was considered a disease-defining/risk-stratifying abnormality in the NOPHO ALL2008 trial because it had been shown to be associated with a worse outcome than HeH and ETV6::RUNX1 in the ALL2000 trial. 12 Despite receiving intensified therapy, the pCIR, pDFS, and pEFS were disappointing; however, most relapses were salvageable, as exemplified by the pOS of 0.97 and by pOS ≥0.92 in a few other trials specifically addressing this aberration (Table 1 and Suppl. Table S10).
Considering the well-established dismal prognosis of iAMP21-positive ALL, 13 this abnormality was risk-stratifying in the NOPHO ALL2008 trial. This notwithstanding, the pCIR, pDFS, and pEFS were unsatisfactory ( Figure 1 and Table 1). Furthermore, although salvage therapy was surprisingly successful, resulting in 5-year pOS rates of 0.92 for both children and adolescents (Suppl. Table S11), both pDFS and pOS kept decreasing with longer follow-up (Suppl. Figure S2), clearly showing that the primary therapy for iAMP21-positive cases needs to be modified.
Because of the notoriously poor outcome of the KMT2A-r, HoL, and NH subtypes (Suppl. Tables S12-S14), these were all stratified as HR. The KMT2A-r-positive cases clearly benefited from this approach-the pEFS/pOS of children (0.77/0.81) and adolescents (0.75/0.88) were not only a substantial improvement compared with the previous ALL2000 trial but also superior to what has been reported by several other study groups (Suppl . Table S12). It is noteworthy that this excellent (for KMT2A-r) outcome of patients of age 1-17 years was achieved by HR chemotherapy alone, not SCT. In contrast, 4 of 8 patients with NH and 5 of 15 HoL patients died (Table 1); thus, improved treatment options are eagerly needed for both these subtypes.
In the multivariable analyses of the BCP ALL patients finally stratified to SR and IR (according to intention-to-treat; Suppl. Table S15), only age and genetic subtypes impacted prognosis, with age >17 years, iAMP21, B-other, and genetically uninformative having a significant negative prognostic impact on pDFS (Suppl . Table S16).
Age was clearly associated with both clinical and genetic features in the NOPHO ALL2008 trial. First, in T-cell ALL, the 5-year pOS decreased by age, being 0.82 for children aged 1-9 years, 0.75 for those aged 10-17 years, and 0.66 for adults (Suppl . Table S3); there was, however, no clear difference in the 5-year pOS between adults of age 18-29 years (0.67) and 30-45 years (0.64). Second, in BCP ALL, the frequencies of the cytogenetic and final risk stratification groups varied among the age groups. The proportions of HeH, ETV6::RUNX1, dic(9;20), NH, and SR decreased by age, whereas KMT2A-r, B-other, genetically unknown, IR, and HR increased by age (Suppl. Tables S17 and S18). Third, adults with KMT2A-r-positive BCP ALL had significantly inferior pCIR (0.40) and pOS (0.41) compared with those aged 1-9 (0.08/0.81) and 10-17 years (0.12/0.88) (P = 0.042 and 0.016, respectively; Suppl. Table S19). Unfortunately, SCT may not be the way forward, except perhaps for KMT2A::AFF1positive cases that are MRD negative at the time of transplantation. 14 Fourth, pDFS, pEFS, and pOS decreased and pCIR increased significantly by age for the patient with B-other ALL (P < 0.001 for all comparisons; Suppl. Table S19). In adult B-other, however, the differences in pDFS, pEFS, pOS, and pCIR between those aged 18-29 years and 30-45 years were not statistically significant (pDFS 0.65/0.57, pEFS 0.65/0.57, pOS 0.77/0.70, and pCIR 0.32/0.40; P > 0.1 for all comparisons). Fifth, the frequencies of genetically uninformative BCP ALLs increased by age, from 3% in children of age 1-9 years to 15% in adults (Suppl. Table S17). The "unknown" group had a relatively poor outcome (Table 1 and Figure 1), but its prognostic impact did differ among the age groups (Suppl. Table S19) or between adults of age 18-29 years and 30-45 years (pEFS 0.76/0.67, pDFS 0.76/0.67, pOS 0.90/0.62, and pCIR 0.30/0.33; P > 0.1 for all comparisons). The general dismal survival of this subtype is not unexpected considering that it most likely includes a mixture of cases with undetected abnormalities, some of which may well confer a poor prognosis. Although genetically uninformative cases obviously occur in all treatment trials, surprisingly little attention has been focused on this groups of patients. The unknown subtype should be investigated in detail and properly addressed in order to make sure that it is kept at a minimum in future treatment trials. Implementing various types of massive parallel sequencing, such as RNA and whole genome sequencing, 15 should hopefully solve the problem because these methods ought to detect all relevant genetic abnormalities. Finally, with regard to age, it is noteworthy that the pDFS, pEFS, and pOS of patients with HeH ALL did not differ significantly among the age groups 1-9, 10-17, and 18-45 years (Suppl . Table S19). Interestingly, the favorable survival of adult HeH, compared to previous trials (Suppl . Table S6), was the result of SR or IR treatment in all cases except one (data not shown).
In conclusion, the survival rates increased for most of the genetic BCP ALL subtypes in the NOPHO ALL2008 trial compared with the previous ALL2000 trial. However, the treatment of older patients and of the subtypes iAMP21 and B-other need be improved, and so does the genetic characterization of the B-other and genetically uninformative groups. To increase survival further, development of targeted therapy for some of the subtypes is clearly needed.